There is continuing disquiet within The Sun about the treatment of its district reporter Jamie Pyatt and its implications for other staff.

That concern has been redoubled by doubts about the paper's future as News International tries to dig itself out of its hacking hole.

More and more staff, past and present - and including very senior executives and respected veterans - are outraged at the conduct of the internal investigation.

Though the sensible ones recognise the need for News Int to clean house, they believe its methods are unjust. To quote one reporter, "it's all too heavy-handed."

They accept that the management and standards committee (MSC) must ensure that Sun journalists were not guilty of illegality, such as hacking or paying police officers.

The Sun would surely benefit from being able to show that its culture is different from that which existed on the News of the World.

But the paper's reporters argue that should lawyers acting for the MSC come across anything that appears to implicate an individual, the person should be given a chance to explain before the material is passed to Scotland Yard.

As the MSC's lawyers go about their work trawling through thousands of emails, there is concern about rough justice being meted out to journalists.

Several members of staff were shocked by the arrest of Pyatt, described to me as "a straightforward and straight district man who is liked by his colleagues." They have registered protests about his treatment.

My understanding is that the matter concerns three payments. But Pyatt contends that none involved police officers and that there is an uncontroversial explanation for each of them.

Pyatt, 48, has been with The Sun since 1987. He is now fuming at home. He was required to hand in his phone and has been told he must now deal only with Wapping's human resources department.

His colleagues feel he has been scapegoated and that there was no need for the company to go to the police without seeking information from him first about the payments.

Some staff also believe that Matt Nixson, The Sun's features editor who was sacked in July, has been poorly treated too.

He previously worked on the News of the World and it was alleged that his dismissal involved his activities there rather than at The Sun.

However, Nixson was not told what evidence against him had been found and, therefore, the exact reason for his being fired. His case was all the more baffling because, in September, the police announced that he would not be arrested, effectively clearing him of wrong-doing.

I have been given information about the reason for his dismissal. It involves a payment though I cannot disclose the details. However, I do know - as the police decision confirms - that it did not involve illegality.

With morale on the floor at The Sun it's no wonder that its editor, Dominic Mohan, thought it necessary to address the troops on Monday.

Evidently, he did well enough, but was undermined yesterday by James Murdoch's equivocation when questioned by the Commons select committee about whether The Sun might be closed in similar fashion to the News of the World.

My hunch is that while Rupert draws breath, The Sun is safe. It turns a profit, unlike The Times and Sunday Times, and was the foundation of his whole media empire.

Affection alone should guarantee its survival unless there is something really nasty in the woodshed, which, to be honest, I rather doubt.